Citation and License

Genome Biology 2012, 13:R42
doi:10.1186/gb-2012-13-6-r42

Published: 14 June 2012

Abstract

Background

To understand the relationship between our bacterial microbiome and health, it is
essential to define the microbiome in the absence of disease. The digestive tract
includes diverse habitats and hosts the human body's greatest bacterial density. We
describe the bacterial community composition of ten digestive tract sites from more
than 200 normal adults enrolled in the Human Microbiome Project, and metagenomically
determined metabolic potentials of four representative sites.

Results

The microbiota of these diverse habitats formed four groups based on similar community
compositions: buccal mucosa, keratinized gingiva, hard palate; saliva, tongue, tonsils,
throat; sub- and supra-gingival plaques; and stool. Phyla initially identified from
environmental samples were detected throughout this population, primarily TM7, SR1,
and Synergistetes. Genera with pathogenic members were well-represented among this
disease-free cohort. Tooth-associated communities were distinct, but not entirely
dissimilar, from other oral surfaces. The Porphyromonadaceae, Veillonellaceae and
Lachnospiraceae families were common to all sites, but the distributions of their
genera varied significantly. Most metabolic processes were distributed widely throughout
the digestive tract microbiota, with variations in metagenomic abundance between body
habitats. These included shifts in sugar transporter types between the supragingival
plaque, other oral surfaces, and stool; hydrogen and hydrogen sulfide production were
also differentially distributed.

Conclusions

The microbiomes of ten digestive tract sites separated into four types based on composition.
A core set of metabolic pathways was present across these diverse digestive tract
habitats. These data provide a critical baseline for future studies investigating
local and systemic diseases affecting human health.